Improvements to the FILTER_QUERY module

phac-nml · May 16, 2024 · df524f6 · df524f6
1 parent 272c8ac
commit df524f6
Showing 1 changed file with 4 additions and 7 deletions.
diff --git a/modules/local/filter/main.nf b/modules/local/filter/main.nf
@@ -13,7 +13,7 @@ process FILTER_QUERY {
     val out_format
 
     output:
-    path("new_addresses.csv"),  emit: csv
+    path("new_addresses.*"),    emit: csv
     path("versions.yml"),       emit: versions
 
     script:
@@ -31,12 +31,9 @@ process FILTER_QUERY {
         ${addresses} \\
         --filter '\$id == \"$queryID\"' \\
         --delimiter "${delimiter}" \\
-        --out-delimiter "${out_delimiter}" \\
-        --out-file ${outputFile}.tmp
-
-    csvtk cut -f 1,2 ${outputFile}.tmp > ${outputFile}.${out_extension}
-    rm ${outputFile}.tmp
-
+        --out-delimiter "${out_delimiter}" | \\
+    csvtk cut -f id,address > ${outputFile}.${out_extension}
+    
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))